- this.av = ap.av;
- this.ap = ap;
- fr = ap.cloneFeatureRenderer();
- }
-
- public void generateHtmlSvgOutput(File file)
- {
- pIndicator = ap.alignFrame;
- pSessionId = System.currentTimeMillis();
- try
- {
- headless = (System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true"));
- if (file == null)
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.waiting_for_user_to_select_output_file", "HTML"));
- JalviewFileChooser chooser = getHTMLChooser();
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle(ap.alignFrame.getTitle());
- chooser.setToolTipText(MessageManager.getString("action.save"));
- int value = chooser.showSaveDialog(ap.alignFrame);
-
- if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
- file = chooser.getSelectedFile();
- ap.alignFrame.repaint();
- }
- else
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "HTML"));
- return;
- }
- }
- } catch (Exception e)
- {
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"), pSessionId);
- e.printStackTrace();
- return;
- }
- final File fileX = file;
- new Thread()
- {
- @Override
- public void run()
- {
- try
- {
- setProgressMessage(null);
- setProgressMessage(MessageManager.formatMessage(
- "status.exporting_alignment_as_x_file", "HTML"));
- AlignmentDimension aDimension = ap.getAlignmentDimension();
- SVGGraphics2D idPanelGraphics = new SVGGraphics2D(
- aDimension.getWidth(),
- aDimension.getHeight());
- SVGGraphics2D alignPanelGraphics = new SVGGraphics2D(
- aDimension.getWidth(),
- aDimension.getHeight());
-
- String renderStyle = jalview.bin.Cache.getDefault(
- "HTML_RENDERING", "Prompt each time");
-
- // If we need to prompt, and if the GUI is visible then
- // Prompt for rendering style
- if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
- {
- HTMLOptions svgOption = new HTMLOptions();
- renderStyle = svgOption.getValue();
-
- if (renderStyle == null || svgOption.cancelled)
- {
- setProgressMessage(MessageManager.formatMessage(
- "status.cancelled_image_export_operation", "HTML"));
- return;
- }
- }
-
- if (renderStyle.equalsIgnoreCase("Lineart"))
- {
- idPanelGraphics.setRenderingHint(SVGHints.KEY_DRAW_STRING_TYPE,
- SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- alignPanelGraphics.setRenderingHint(
- SVGHints.KEY_DRAW_STRING_TYPE,
- SVGHints.VALUE_DRAW_STRING_TYPE_VECTOR);
- }
- if (av.getWrapAlignment())
- {
- printWrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
- alignPanelGraphics);
- }
- else
- {
- printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
- idPanelGraphics, alignPanelGraphics);
- }
-
- String idPanelSvgData = idPanelGraphics.getSVGDocument();
- String alignPanelSvgData = alignPanelGraphics.getSVGDocument();
- String jsonData = null;
- boolean isEmbbedBioJSON = Boolean.valueOf(jalview.bin.Cache
- .getDefault("EXPORT_EMBBED_BIOJSON", "true"));
- if (isEmbbedBioJSON)
- {
- AlignExportSettingI exportSettings = new AlignExportSettingI()
- {
- @Override
- public boolean isExportHiddenSequences()
- {
- return true;
- }
-
- @Override
- public boolean isExportHiddenColumns()
- {
- return true;
- }
-
- @Override
- public boolean isExportAnnotations()
- {
- return true;
- }
-
- @Override
- public boolean isExportFeatures()
- {
- return true;
- }
-
- @Override
- public boolean isExportGroups()
- {
- return true;
- }
-
- @Override
- public boolean isCancelled()
- {
- return false;
- }
-
- };
- AlignmentExportData exportData = jalview.gui.AlignFrame
- .getAlignmentForExport(JSONFile.FILE_DESC, av,
- exportSettings);
- jsonData = new FormatAdapter(ap, exportData.getSettings())
- .formatSequences(JSONFile.FILE_DESC,
- exportData.getAlignment(),
- exportData.getOmitHidden(),
- exportData.getStartEndPostions(),
- av.getColumnSelection());
- }
- String htmlData = getHtml(idPanelSvgData, alignPanelSvgData, jsonData,
- av.getWrapAlignment());
- FileOutputStream out = new FileOutputStream(fileX);
- out.write(htmlData.getBytes());
- out.flush();
- out.close();
- if (!(System.getProperty("java.awt.headless") != null && System
- .getProperty("java.awt.headless").equals("true")))
- {
- jalview.util.BrowserLauncher.openURL("file:///" + fileX);
- }
- } catch (OutOfMemoryError err)
- {
- System.out.println("########################\n"
- + "OUT OF MEMORY " + fileX + "\n"
- + "########################");
- new OOMWarning("Creating Image for " + fileX, err);
- } catch (Exception e)
- {
- e.printStackTrace();
- pIndicator.setProgressBar(MessageManager.formatMessage(
- "info.error_creating_file", "HTML"), pSessionId);
- }
- setProgressMessage(MessageManager.formatMessage(
- "status.export_complete", "HTML"));
- }
- }.start();
-
- }
-
- private void setProgressMessage(String message)
- {
- if (pIndicator != null && !headless)
- {
- pIndicator.setProgressBar(message, pSessionId);
- }
- else
- {
- System.out.println(message);
- }